Systemic autoimmune diseases are characterized by their heterogenic clinical presentations and often poorly understood pathogenesis. As such, the diagnosis process may be complex and the final diagnosis is made by an expert, after considering a differential diagnosis. Classification criteria are developed for research purposes to select homogenous populations of already diagnosed patients. In clinical practice, these classification criteria are sometimes misused as diagnostic criteria. We describe three patient histories. Two patients met the classification criteria of several separate diseases, emphasizing the amount of overlap between different sets of criteria and the necessity of making a diagnosis before using classification criteria. A third patient was diagnosed with systemic sclerosis and later developed rheumatoid arthritis; a diagnosis that could have been overlooked if classification criteria were used diagnostically. We describe the correct use of classification criteria in systemic autoimmune diseases and discuss what the diagnostic process is supposed to entail.